Tags » Bioinformatics

Assignment story: The CALM1 gene

I recently looked at my personal blog and saw that I had an unpublished blog post there that contained a bunch of screenshots and had only one sentence incomplete sentence: 419 more words



Bu sene ISCB-SC-RSG Türkiye grubu olarak 5.sini gerçekleştirdiğimiz öğrenci sempozyumumuzun detaylarını sizinle paylaşmaktan mutluluk duyuyoruz!

Öğrenci sempozyumumuz 25-27 Ekim tarihleri arasında gerçekleşen HIBIT 2018’in 3.gününde Falez Uygulama Oteli’nde harika bir katılımla gerçekleşti.  818 more words


(Reblog) A Tale of Two Cohorts

Original posting on BioBE.

Sequence data contamination from biological or digital sources can obscure true results and falsely raise one’s hopes.  Contamination is a persist issue in microbial ecology, and each experiment faces unique challenges from a myriad of sources, which I have  1,756 more words

Lab Work

Implementing the Epigraph algorithm with Integer Programming

I’ve been meaning to try to replicate this paper for a while: https://www.nature.com/articles/srep33987. It presents the epigraph algorithm, which is short for “epitope graph”. Basically, it slices a set of proteins up into k-mers, then constructs a graph, where each unique k-mer is a node. 248 more words


The ‘-max_target_seqs’ parameter of NCBI BLAST may not do what you think it does

In September, Shah et al published an article in Bioinformatics pointing out a widespread misunderstanding of one of the parameters of NCBI BLAST. The sensitivity of BLAST means it can be time-consuming to run. 279 more words